Diagnostic Report – based on current model outputs - combined all settings
202310gavi-4 – central burden estimates
JHU-Lee Modeling Group
2024-03-27 09:23:16.610883
Table 1. The Model Specs
Specific characteristics of this model are shown in this table.
| Item | Details |
|---|---|
| Disease | Cholera |
| ModelingGroup | JHU-Lee |
| YearRange | 2000-2100 |
| AgeRange | 0-100 |
| CountryList | AFG - AGO - BDI - BEN - BFA - BGD - CAF - CIV - CMR - COD - COG - DZA - ETH - GHA - GIN - GNB - HTI - IND - IRN - IRQ - KEN - LBR - MDG - MLI - MOZ - MRT - MWI - NAM - NER - NGA - NPL - PAK - PHL - RWA - SEN - SLE - SOM - SSD - TCD - TGO - THA - TZA - UGA - YEM - ZAF - ZMB - ZWE |
| SimulatedOutcomes | cohort_size - cases - deaths - dalys - yll |
Coverage Trajectories
The trends of the specific coverage sets per campaign scenario can be observed in this figure. For the ocv1-ocv2-default scenario, the coverage reported here is the adjusted coverage from montagu, which is modified to consider the fact that there is no correlation between rounds ‘OCV1’ and ‘OCV2’.
Figure 1. Modified montagu coverage per vaccination scenario
Ocv1-default
Ocv1-ocv2-default
Figure 2. Comparison of modelled and montagu Vaccinated People (VP) for each campaign scenario
Modelled number of vaccinated people and the number of vaccinated people per country/year as calculated using the coverage tables from montagu. Note that there could be cases where the modelled number of vaccinated people can me different from the number of vaccinated people calculated using the montagu data.
Ocv1-default Scenario
Ocv1-ocv2-default Scenario
## Warning: Removed 4 rows containing missing values (`geom_bar()`).
Table 2. Check that the number of people vaccinated with at least one dose in the ocv1-ocv2-scenario (the sum of vaccinated people with one and two doses) is higher than the number of people who reveived either round ‘OCV1’ or round ‘OCV2’
This only applies to the ocv1-ocv2 scenario and uses the unadjusted montagu coverage to calculate the number of people vaccinated at rounds ‘OCV1’ and ‘OCV2’ and the adjusted montagu coverage to calculate the number of people who received at least one dose of the vaccine. In the table below, we show only cases where the number of people vaccinated with at least one dose is higher than the number of people who reveived either round ‘OCV1’ or round ‘OCV2’
## Joining with `by = join_by(country_code, year)`| country_code | year | OCV1 | OCV2 | vp_at_least_one_dose |
|---|---|---|---|---|
| BGD | 2028 | 66510937 | 54773713 | 18702819 |
| BGD | 2034 | 69772263 | 57459510 | 19619902 |
| BGD | 2040 | 72299706 | 59540934 | 20330617 |
| CMR | 2028 | 10481268 | 8631632 | 6063503 |
| CMR | 2034 | 12068206 | 9938523 | 6981558 |
| CMR | 2040 | 13746073 | 11320295 | 7952214 |
| GHA | 2028 | 12529545 | 10318449 | 6273129 |
| GHA | 2034 | 13900462 | 11447439 | 6959502 |
| GHA | 2040 | 15297706 | 12598111 | 7659057 |
| GNB | 2028 | 883961 | 727968 | 224804 |
| GNB | 2034 | 994385 | 818906 | 252886 |
| GNB | 2040 | 1106027 | 910846 | 281279 |
| MDG | 2025 | 26256159 | 21622719 | 24711677 |
| MDG | 2031 | 30102928 | 24790646 | 28332166 |
| MDG | 2037 | 34093390 | 28076909 | 32087897 |
| RWA | 2025 | 12182419 | 10032580 | 11465805 |
| RWA | 2031 | 13840888 | 11398379 | 13026717 |
| RWA | 2037 | 15530964 | 12790206 | 14617379 |
| SEN | 2025 | 15406375 | 12687603 | 14500122 |
| SEN | 2031 | 17869234 | 14715840 | 16818105 |
| SEN | 2037 | 20561411 | 16932927 | 19351920 |
| SOM | 2031 | 8552975 | 7043627 | 2076708 |
| SOM | 2037 | 10081598 | 8302493 | 2447865 |
| TCD | 2028 | 6173631 | 5084166 | 4951200 |
| TCD | 2034 | 7310022 | 6020018 | 5862576 |
| TCD | 2040 | 8540420 | 7033287 | 6849348 |
| ZAF | 2025 | 51486116 | 42400331 | 48457517 |
| ZAF | 2031 | 54525478 | 44903335 | 51318098 |
| ZAF | 2037 | 57151237 | 47065725 | 53789401 |
Table 3. Coverage Data Check for Campaign Scenario
Age ranges of the different coverage sets include either standard age ranges (as it is the case of Measles) but sometimes it differs by year and country so that several combinations can be possible (See table below).
| coverage_set_name | age_from | age_to | freq |
|---|---|---|---|
| cholera-ocv1-default | 1 | 100 | 309 |
| coverage_set_name | age_from | age_to | freq |
|---|---|---|---|
| cholera-ocv1-ocv2-default | 1 | 100 | 618 |
Figure 3. Vaccinated People
The estimates of vaccinated people (VP) are obtained by multiplying coverage from each coverage set in Montagu (after adjustment for the ocv1-ocv2-default scenario) and the target population. The following graphs show the number of Vaccinated People (VP) at a global level by scenario.
Table 4. Check the general info
Expected number of rows.
| scenario_description | outcome_code | number_of_non_na_rows |
|---|---|---|
| Campaign, ocv1-Default | cohort_size | 479447 |
| Campaign, ocv1-Default | cases | 479447 |
| Campaign, ocv1-Default | deaths | 479447 |
| Campaign, ocv1-Default | dalys | 479447 |
| Campaign, ocv1-Default | yll | 479447 |
| No vaccination | cohort_size | 479447 |
| No vaccination | cases | 479447 |
| No vaccination | deaths | 479447 |
| No vaccination | dalys | 479447 |
| No vaccination | yll | 479447 |
| scenario_description | outcome_code | number_of_non_na_rows |
|---|---|---|
| Campaign, ocv2-Default | cohort_size | 479447 |
| Campaign, ocv2-Default | cases | 479447 |
| Campaign, ocv2-Default | deaths | 479447 |
| Campaign, ocv2-Default | dalys | 479447 |
| Campaign, ocv2-Default | yll | 479447 |
| No vaccination | cohort_size | 479447 |
| No vaccination | cases | 479447 |
| No vaccination | deaths | 479447 |
| No vaccination | dalys | 479447 |
| No vaccination | yll | 479447 |
Figure 4. Missing Value Check
This figure shows the shape of the upload by scenarios and outcomes (whether there are missing values, 1 means no missing value).
Figure 5. Positive Value Check
This figure shows the pattern of positive values (number of positive values across all simulated countries).
Figure 6. Check the cohort size – Global
Notion: the interpolated population dataset doesn’t have info for age 100 but has the above, we will leave that out to keep the consistency.
This figure shows the comparison of cohort size against interpolated population in all countries.
Figure 7. Check the Cohort Size – All Simulated Countries
This figure shows the comparison of cohort size against interpolated population in the simulated countries.
Table 5. Cohort Size Check in Table Format – All Countries (not included in this report)
Table 6. Cohort Size Check in Table Format – Each Country (not included in this report)
Figure 8. Age Distribution for Different Estimates
This figure shows the aggregated (for all countries) age distribution patterns by outcome.
Figure 9. Global Burden Comparison in 2000-2030.
This figure shows the global (simulated countries) burden values by decades 2000-2030.
Figure 10. Global Burden Comparison in 2000-2100.
This figure shows the global (simulated countries) burden disease values 2000-2100.
Figure 11. Case Estimates for Each Country across Scenarios
This figure shows every single simulated countries’ estimated case values and differences 2000-2100.
Figure 12. Death Estimates for Each Country across Scenarios
This figure shows every single simulated countries’ estimated deaths values and differences 2000-2100.
